Starting phenix.real_space_refine on Sat Aug 3 12:41:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w87_37347/08_2024/8w87_37347_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5235 2.51 5 N 1415 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 224": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "R ASP 21": "OD1" <-> "OD2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8228 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1906 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'B40': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.58 Number of scatterers: 8228 At special positions: 0 Unit cell: (82.4, 98.88, 132.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1515 8.00 N 1415 7.00 C 5235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.26 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.6 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B40 R 501 " Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 44.2% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 33 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.934A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.511A pdb=" N PHE A 222 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 239 through 253 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.749A pdb=" N ILE A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 365 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.524A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.812A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 87 Processing helix chain 'R' and resid 91 through 127 removed outlier: 4.282A pdb=" N PHE R 95 " --> pdb=" O PHE R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 231 removed outlier: 3.990A pdb=" N LEU R 231 " --> pdb=" O ALA R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 278 removed outlier: 3.610A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 284 through 305 removed outlier: 3.631A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 198 removed outlier: 4.685A pdb=" N VAL A 208 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N GLY A 47 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 227 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 228 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N PHE A 264 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 230 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN A 266 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL A 232 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.944A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.743A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.556A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.839A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.840A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.851A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1386 1.32 - 1.44: 2303 1.44 - 1.57: 4625 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 8406 Sorted by residual: bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.334 1.415 -0.082 1.23e-02 6.61e+03 4.39e+01 bond pdb=" C ASP R 103 " pdb=" N ILE R 104 " ideal model delta sigma weight residual 1.334 1.258 0.076 1.25e-02 6.40e+03 3.74e+01 bond pdb=" C ASP R 103 " pdb=" O ASP R 103 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.15e-02 7.56e+03 9.89e+00 bond pdb=" CB ASP R 103 " pdb=" CG ASP R 103 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.29e+00 bond pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 1.530 1.557 -0.027 1.57e-02 4.06e+03 3.05e+00 ... (remaining 8401 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 222 107.21 - 113.94: 4701 113.94 - 120.67: 3468 120.67 - 127.39: 2904 127.39 - 134.12: 89 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C ASP R 103 " pdb=" CA ASP R 103 " pdb=" CB ASP R 103 " ideal model delta sigma weight residual 110.96 105.05 5.91 1.54e+00 4.22e-01 1.47e+01 angle pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sigma weight residual 115.05 104.23 10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" C B40 R 501 " ideal model delta sigma weight residual 114.49 104.29 10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 108.63 3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" N SER B 331 " pdb=" CA SER B 331 " pdb=" C SER B 331 " ideal model delta sigma weight residual 108.60 112.56 -3.96 1.46e+00 4.69e-01 7.37e+00 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.64: 4508 19.64 - 39.29: 381 39.29 - 58.93: 79 58.93 - 78.58: 16 78.58 - 98.22: 6 Dihedral angle restraints: 4990 sinusoidal: 1945 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CB B40 R 501 " pdb=" N B40 R 501 " pdb=" CA B40 R 501 " pdb=" CM B40 R 501 " ideal model delta sinusoidal sigma weight residual 168.08 -93.70 -98.22 1 3.00e+01 1.11e-03 1.22e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1106 0.056 - 0.113: 144 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA B40 R 501 " pdb=" N B40 R 501 " pdb=" C B40 R 501 " pdb=" CB B40 R 501 " both_signs ideal model delta sigma weight residual False -2.42 -2.71 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP R 103 " pdb=" N ASP R 103 " pdb=" C ASP R 103 " pdb=" CB ASP R 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1272 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 284 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C THR R 284 " -0.059 2.00e-02 2.50e+03 pdb=" O THR R 284 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU R 285 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 282 " 0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO R 283 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.182 9.50e-02 1.11e+02 8.20e-02 4.90e+00 pdb=" NE ARG B 19 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.002 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 594 2.73 - 3.28: 8380 3.28 - 3.82: 13939 3.82 - 4.36: 17219 4.36 - 4.90: 30105 Nonbonded interactions: 70237 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.193 3.040 nonbonded pdb=" O ASN A 188 " pdb=" OG SER A 189 " model vdw 2.226 3.040 nonbonded pdb=" C B40 R 501 " pdb=" CM B40 R 501 " model vdw 2.251 3.104 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.314 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.319 3.040 ... (remaining 70232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8406 Z= 0.217 Angle : 0.561 10.817 11384 Z= 0.318 Chirality : 0.041 0.282 1275 Planarity : 0.005 0.083 1448 Dihedral : 15.674 98.222 3019 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.45 % Allowed : 16.10 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 1031 helix: 2.26 (0.25), residues: 416 sheet: 0.46 (0.34), residues: 228 loop : -0.01 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 291 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 70 TYR 0.008 0.001 TYR A 313 ARG 0.015 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7653 (mtm110) REVERT: B 17 GLN cc_start: 0.6251 (tt0) cc_final: 0.6005 (tm130) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 1.3037 time to fit residues: 179.5306 Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 239 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8406 Z= 0.188 Angle : 0.527 6.456 11384 Z= 0.287 Chirality : 0.042 0.157 1275 Planarity : 0.004 0.065 1448 Dihedral : 5.454 57.502 1149 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.14 % Allowed : 14.08 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1031 helix: 2.36 (0.25), residues: 415 sheet: 0.55 (0.36), residues: 213 loop : 0.10 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.004 0.001 HIS G 44 PHE 0.021 0.001 PHE R 165 TYR 0.031 0.001 TYR R 27 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8927 (mttp) cc_final: 0.8606 (mmtm) REVERT: A 213 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7948 (p0) REVERT: A 318 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 321 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7443 (mtm-85) REVERT: A 355 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8267 (t0) REVERT: B 214 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.7586 (mpp80) REVERT: B 243 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8374 (p) REVERT: R 80 SER cc_start: 0.8040 (t) cc_final: 0.7246 (p) outliers start: 19 outliers final: 7 residues processed: 151 average time/residue: 1.2680 time to fit residues: 203.0787 Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8406 Z= 0.263 Angle : 0.535 6.549 11384 Z= 0.290 Chirality : 0.043 0.157 1275 Planarity : 0.004 0.058 1448 Dihedral : 5.263 55.929 1148 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 15.20 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1031 helix: 2.17 (0.25), residues: 421 sheet: 0.46 (0.36), residues: 215 loop : 0.04 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 218 HIS 0.004 0.001 HIS G 44 PHE 0.014 0.002 PHE B 292 TYR 0.010 0.001 TYR A 313 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.8933 (mttp) cc_final: 0.8613 (mmtm) REVERT: A 355 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8295 (t0) REVERT: B 251 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8502 (mtt-85) REVERT: R 80 SER cc_start: 0.8038 (t) cc_final: 0.7219 (p) outliers start: 21 outliers final: 11 residues processed: 154 average time/residue: 1.3005 time to fit residues: 211.7370 Evaluate side-chains 144 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8406 Z= 0.224 Angle : 0.507 6.032 11384 Z= 0.275 Chirality : 0.042 0.152 1275 Planarity : 0.004 0.055 1448 Dihedral : 5.211 57.042 1148 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.27 % Allowed : 16.33 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1031 helix: 2.18 (0.25), residues: 421 sheet: 0.45 (0.36), residues: 215 loop : 0.00 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.001 PHE R 165 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7976 (mptt) REVERT: A 200 LYS cc_start: 0.8934 (mttp) cc_final: 0.8612 (mmtm) REVERT: A 213 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7700 (p0) REVERT: A 321 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7561 (mtm-85) REVERT: A 330 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7433 (mtm110) REVERT: A 355 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8299 (t0) REVERT: B 175 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: B 214 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7824 (mpp80) REVERT: R 23 ARG cc_start: 0.6267 (OUTLIER) cc_final: 0.5551 (ptt90) REVERT: R 135 MET cc_start: 0.8863 (mmp) cc_final: 0.8533 (mmt) outliers start: 29 outliers final: 16 residues processed: 155 average time/residue: 1.2750 time to fit residues: 209.4963 Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8406 Z= 0.168 Angle : 0.475 5.814 11384 Z= 0.258 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.054 1448 Dihedral : 4.920 55.709 1148 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.82 % Allowed : 17.23 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1031 helix: 2.29 (0.25), residues: 422 sheet: 0.52 (0.36), residues: 215 loop : 0.03 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 218 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE A 196 TYR 0.010 0.001 TYR N 95 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7676 (tmtt) REVERT: A 200 LYS cc_start: 0.8926 (mttp) cc_final: 0.8621 (mmtm) REVERT: A 213 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 330 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7434 (mtm110) REVERT: A 355 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8304 (t0) REVERT: B 175 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: R 23 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5521 (ptt90) outliers start: 25 outliers final: 12 residues processed: 158 average time/residue: 1.2083 time to fit residues: 202.6730 Evaluate side-chains 149 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8406 Z= 0.152 Angle : 0.467 5.597 11384 Z= 0.254 Chirality : 0.041 0.146 1275 Planarity : 0.004 0.053 1448 Dihedral : 4.773 55.786 1148 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.27 % Allowed : 17.68 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1031 helix: 2.37 (0.25), residues: 422 sheet: 0.51 (0.36), residues: 217 loop : 0.05 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE R 165 TYR 0.014 0.001 TYR R 27 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7661 (tmtt) REVERT: A 200 LYS cc_start: 0.8919 (mttp) cc_final: 0.8634 (mmtt) REVERT: A 213 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7664 (p0) REVERT: A 330 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7345 (mtm110) REVERT: A 355 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8306 (t0) REVERT: B 17 GLN cc_start: 0.6536 (tt0) cc_final: 0.6269 (tm130) REVERT: R 23 ARG cc_start: 0.6356 (OUTLIER) cc_final: 0.5539 (ptt90) outliers start: 29 outliers final: 16 residues processed: 156 average time/residue: 1.1688 time to fit residues: 194.1915 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.0010 overall best weight: 0.7488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8406 Z= 0.161 Angle : 0.473 6.370 11384 Z= 0.256 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.068 1448 Dihedral : 4.731 54.965 1148 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.15 % Allowed : 18.02 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 1031 helix: 2.41 (0.25), residues: 422 sheet: 0.50 (0.36), residues: 217 loop : 0.04 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE A 196 TYR 0.013 0.001 TYR R 279 ARG 0.015 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7671 (tmtt) REVERT: A 200 LYS cc_start: 0.8917 (mttp) cc_final: 0.8633 (mmtt) REVERT: A 213 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7640 (p0) REVERT: A 355 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8307 (t0) REVERT: B 17 GLN cc_start: 0.6529 (tt0) cc_final: 0.6185 (tm130) REVERT: R 23 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5537 (ptt90) outliers start: 28 outliers final: 16 residues processed: 155 average time/residue: 1.2182 time to fit residues: 200.3905 Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 43 ILE Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8406 Z= 0.166 Angle : 0.481 6.620 11384 Z= 0.260 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.070 1448 Dihedral : 4.714 54.809 1148 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.15 % Allowed : 18.36 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.27), residues: 1031 helix: 2.41 (0.25), residues: 422 sheet: 0.57 (0.36), residues: 215 loop : -0.01 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE A 196 TYR 0.014 0.001 TYR R 279 ARG 0.018 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7661 (tmtt) REVERT: A 200 LYS cc_start: 0.8919 (mttp) cc_final: 0.8634 (mmtt) REVERT: A 213 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7620 (p0) REVERT: A 330 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7528 (mtm110) REVERT: A 355 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8298 (t0) REVERT: B 17 GLN cc_start: 0.6539 (tt0) cc_final: 0.6260 (tm130) REVERT: N 46 GLU cc_start: 0.8339 (tt0) cc_final: 0.8080 (pt0) REVERT: N 108 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: R 23 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5515 (ptt90) outliers start: 28 outliers final: 15 residues processed: 151 average time/residue: 1.2234 time to fit residues: 196.1714 Evaluate side-chains 150 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8406 Z= 0.189 Angle : 0.492 7.041 11384 Z= 0.266 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.079 1448 Dihedral : 4.701 54.804 1148 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.93 % Allowed : 18.36 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1031 helix: 2.36 (0.25), residues: 422 sheet: 0.49 (0.36), residues: 217 loop : 0.02 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 218 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 196 TYR 0.014 0.001 TYR R 279 ARG 0.019 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7686 (tmtt) REVERT: A 200 LYS cc_start: 0.8926 (mttp) cc_final: 0.8609 (mmtt) REVERT: A 213 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 355 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8294 (t0) REVERT: B 214 ARG cc_start: 0.8278 (tpp80) cc_final: 0.8060 (mmm-85) REVERT: N 46 GLU cc_start: 0.8349 (tt0) cc_final: 0.8089 (pt0) REVERT: N 108 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: R 23 ARG cc_start: 0.6358 (OUTLIER) cc_final: 0.5518 (ptt90) outliers start: 26 outliers final: 14 residues processed: 151 average time/residue: 1.1990 time to fit residues: 192.2283 Evaluate side-chains 146 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8406 Z= 0.179 Angle : 0.498 6.469 11384 Z= 0.270 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.058 1448 Dihedral : 4.511 54.777 1146 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.14 % Allowed : 19.26 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1031 helix: 2.32 (0.25), residues: 421 sheet: 0.54 (0.36), residues: 215 loop : -0.01 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE R 154 TYR 0.014 0.001 TYR R 279 ARG 0.012 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7722 (tmtt) REVERT: A 200 LYS cc_start: 0.8919 (mttp) cc_final: 0.8603 (mmtt) REVERT: A 213 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7586 (p0) REVERT: A 355 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8285 (t0) REVERT: B 17 GLN cc_start: 0.6553 (tt0) cc_final: 0.6283 (tm130) REVERT: B 214 ARG cc_start: 0.8252 (tpp80) cc_final: 0.8031 (mmm-85) REVERT: N 46 GLU cc_start: 0.8362 (tt0) cc_final: 0.8103 (pt0) REVERT: R 23 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.5504 (ptm-80) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 1.2796 time to fit residues: 199.6307 Evaluate side-chains 147 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain R residue 23 ARG Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.106517 restraints weight = 9307.336| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.31 r_work: 0.3123 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8406 Z= 0.181 Angle : 0.500 7.553 11384 Z= 0.273 Chirality : 0.041 0.147 1275 Planarity : 0.004 0.080 1448 Dihedral : 4.509 54.811 1146 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.36 % Allowed : 19.71 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1031 helix: 2.30 (0.25), residues: 422 sheet: 0.53 (0.36), residues: 215 loop : -0.00 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.012 0.001 PHE R 154 TYR 0.013 0.001 TYR R 279 ARG 0.021 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.53 seconds wall clock time: 64 minutes 56.63 seconds (3896.63 seconds total)